1521-0081/71/2/170–197$35.00 https://doi.org/10.1124/pr.117.015370 PHARMACOLOGICAL REVIEWS Pharmacol Rev 71:170–197, April 2019 Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY Attribution 4.0 International license. ASSOCIATE EDITOR: QIANG MA A Practical Review of Proteasome Pharmacology Tiffany A. Thibaudeau and David M. Smith Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia Abstract ....................................................................................171 I. Introduction . ..............................................................................171 II. Proteasome Structure and Function . ......................................................173 A. Proteasome Structure and Activity ......................................................173 1. Active Sites of the 20S Proteasome. ................................................174 2. Specialized Catalytic Subunits . ......................................................174 3. Proteasome Regulatory Caps and Their Diverse Biologic Roles........................175 B. Proteasome-Dependent Cellular Processes ...............................................176 1. Cell Cycle . ........................................................................177 2. Nuclear Factor-kB Activation . ......................................................177 3. Neuronal Function. ..................................................................177 Downloaded from 4. Endoplasmic Reticulum–Associated Protein Degradation and the Unfolded Protein Response ............................................................................178 III. Development of Proteasome Inhibitors ......................................................178 A. The Rise of Proteasome Inhibitors . ......................................................178 B. Chemical Classes of Proteasome Inhibitors ..............................................179 1. Peptide Aldehydes . ..................................................................179 by guest on September 30, 2021 2. Peptide Boronates . ..................................................................179 3. Epoxomicin and Epoxyketones . ......................................................179 4. Lactacystin and b-Lactone ...........................................................179 5. Vinyl Sulfones .......................................................................181 C. Considerations for Proteasome Inhibitor Design .........................................181 1. Substrate Binding Pockets ...........................................................181 2. Structural Analysis of Bound Inhibitors ..............................................181 3. Proteasome Inhibitor Pharmacophore Properties .....................................182 IV. Methods for Pharmacological Proteasome Research..........................................182 A. Proteasome Purifications ................................................................182 1. Endogenous Proteasome Purification . ................................................182 2. Affinity-Tagged Proteasomes . ......................................................183 3. Immunoproteasomes.................................................................183 4. Validating and Storing Proteasome Preparations .....................................183 B. Monitoring Proteasome Activity . ......................................................184 1. Peptide-Based Model Substrates .....................................................184 2. Protein-Based Model Substrates .....................................................184 a. Methods to quantitate protein degradation . .....................................184 b. 20S (19S-independent) substrates. ................................................185 c. 26S (ubiquitin-independent) substrates . ..........................................185 d. 26S (ubiquitin-dependent) substrates . ..........................................186 3. Proteasome Activity in Cell Culture . ................................................186 4. In Vivo Proteasome Activity . ......................................................186 C. Proteasome Active Site Probes ..........................................................186 Address correspondence to: Dr. David M. Smith, Department of Biochemistry, West Virginia University School of Medicine, Blanchette Rockefeller Neurosciences Institute, WVU Cancer Institute, 64 Medical Center Dr., Morgantown, WV 26506. E-mail: [email protected]. This work was supported by the National Institutes of Health [Grant R01GM107129]. https://doi.org/10.1124/pr.117.015370. 170 A Practical Review of Proteasome Pharmacology 171 V. Proteasome Inhibitors to Treat Human Disease . ..........................................187 A. Hematologic Malignancies. ............................................................187 1. Bortezomib and Multiple Myeloma . ................................................187 2. Bortezomib Resistance . ............................................................187 3. Bortezomib Dose-Limiting Toxicity . ................................................188 4. Bortezomib Efficacy in Solid Tumors . ................................................188 B. Second-Generation Proteasome Inhibitors ...............................................188 1. Carfilzomib . ........................................................................189 2. Ixazomib ............................................................................189 C. Additional Proteasome Inhibitors in Clinical Trials . .....................................189 1. Marizomib. ........................................................................189 2. Oprozomib. ........................................................................190 D. Immunoproteasome-Specific Proteasome Inhibitors . .....................................190 E. Novel Combination Therapies ...........................................................191 VI. Novel Proteasome Drug Targets. ............................................................191 A. Deubiquitinating Enzyme Inhibitors.....................................................191 B. Activation of 20S by Gate Opening ......................................................192 VII. Conclusions . ..............................................................................192 Acknowledgments . ........................................................................192 References..................................................................................193 Abstract——The ubiquitin proteasome system (UPS) suppressors and cell cycle checkpoint inhibitors neces- degrades individual proteins in a highly regulated fash- sary for rapid cell division. Thus, proteasome inhibitors ion and is responsible for the degradation of misfolded, have proven clinically useful to treat some types of damaged, or unneeded cellular proteins. During the past cancer, especially multiple myeloma. Numerous cellular 20 years, investigators have established a critical role for processes rely on finely tuned proteasome function, the UPS in essentially every cellular process, including making it a crucial target for future therapeutic inter- cell cycle progression, transcriptional regulation, genome vention in many diseases, including neurodegenerative integrity, apoptosis, immune responses, and neuronal diseases, cystic fibrosis, atherosclerosis, autoimmune plasticity. At the center of the UPS is the proteasome, a diseases, diabetes, and cancer. In this review, we discuss large and complex molecular machine containing a multi- the structure and function of the proteasome, the mech- catalytic protease complex. When the efficiency of this anisms of action of different proteasome inhibitors, proteostasis system is perturbed, misfolded and damaged various techniques to evaluate proteasome function protein aggregates can accumulate to toxic levels and in vitro and in vivo, proteasome inhibitors in preclinical cause neuronal dysfunction, which may underlie many and clinical development, and the feasibility for pharma- neurodegenerative diseases. In addition, many cancers cological activation of the proteasome to potentially treat rely on robust proteasome activity for degrading tumor neurodegenerative disease. I. Introduction proteins functioned primarily as energy, providing fuel Early biologists viewed cellular proteins as essen- for the body. Rudolf Schoenheimer and colleagues tially stable constituents subjected to only minor “wear challenged that notion in the late 1930s, using stable and tear.” The widely accepted theory was that dietary isotopes to show that trace dietary amino acids rapidly ABBREVIATIONS: ABP, activity-based probe; amc, amino‐4‐methylcoumarin; AsnEDA, asparagine-ethylenediamine; BMSC, bone marrow stem cell; CNS, central nervous system; DRG, dorsal root ganglion; DUB, deubiquitinase; E-64, (2S,3S)-3-[[(2S)-1-[4-(diaminomethylideneamino)- butylamino]-4-methyl-1-oxopentan-2-yl]carbamoyl]oxirane-2-carboxylic acid; EM, electron microscopy; ER, endoplasmic reticulum; ERAD, endoplasmic reticulum–associated protein degradation; FDA, U.S.FoodandDrugAdministration;GBM,glioblastoma;GFP,greenfluorescent protein; GST, glutathione S-transferase; HbYX, hydrophobic-tyrosine-any residue; HEK293, human embryonic kidney 293; IFN, interferon; IKK, IkB kinase; KZR-616, (2S,3R)-N-((S)-3-(cyclopent-1-en-1-yl)-1-((R)-2-methyloxiran-2-yl)-1-oxopropan-2-yl)-3-hydroxy-3-(4-methoxyphenyl)-2-((S)-2-(2- morpholinoacetamido)propanamido)propanamide;